Molecular Dynamics of Variegated Polyamide Dendrimers

We have used molecular dynamics simulations to study the structures of a range of heterogeneously functionalized (“variegated”) dendrimers and the distributions in space of their caps. By a virtual capping approach, we compare an asymmetric dendrimer (dendritic poly(l-lysine), PLL) and a symmetric polyamide (SPAM) dendrimer. SPAM is larger and more spherical than PLL, and its caps are more evenly distributed throughout the molecule. Protonation of an amine-capped dendrimer causes substantial swelling. The distribution of caps relative to each other is strongly affected by conformational change. Simulation of a SPAM framework with chemically distinct caps shows that whole-dendrimer properties are largely unaffected by the topological arrangement of the caps. Using both modeling approaches, we found that differentiation at the dendrimer’s core produces strongly dipolar dendrimers, while differentiation between branches in the outermost generation produces largely nonpolar dendrimers, with a gradual transition between these extremes. The effect of variegation topology on spatial distribution of caps is modified by the interactions between the caps (particularly electrostatic interactions) and with other species in the environment.